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- PDB-1dvb: RUBRERYTHRIN -

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Basic information

Entry
Database: PDB / ID: 1dvb
TitleRUBRERYTHRIN
ComponentsRUBRERYTHRIN
KeywordsELECTRON TRANSPORT / IRON / FERROXIDASE
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding / cytoplasm
Similarity search - Function
: / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Ferritin, core subunit, four-helix bundle / Ferritin ...: / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Single Sheet / Ferritin-like superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDesulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / COORDINATES FROM PDB / Resolution: 1.9 Å
AuthorsSieker, L.C. / Holmes, M. / Le Trong, I. / Turley, S. / Liu, M.Y. / Legall, J. / Stenkamp, R.E.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2000
Title: The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results.
Authors: Sieker, L.C. / Holmes, M. / Le Trong, I. / Turley, S. / Liu, M.Y. / LeGall, J. / Stenkamp, R.E.
History
DepositionJan 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUBRERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7544
Polymers21,5771
Non-polymers1773
Water2,972165
1
A: RUBRERYTHRIN
hetero molecules

A: RUBRERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5098
Polymers43,1552
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3460 Å2
ΔGint-60 kcal/mol
Surface area18100 Å2
MethodPISA
2
A: RUBRERYTHRIN
hetero molecules

A: RUBRERYTHRIN
hetero molecules

A: RUBRERYTHRIN
hetero molecules

A: RUBRERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01816
Polymers86,3094
Non-polymers70812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12730 Å2
ΔGint-156 kcal/mol
Surface area30400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.630, 81.550, 100.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein RUBRERYTHRIN


Mass: 21577.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / References: UniProt: P24931
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: PEG4000, Tris acid maleate, pH 7.5, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: deMare, F., (1996) Nat. Struct. Biol., 3, 539.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTRIZMA hydrochloride1reservoir
215 %PEG14501reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 226047 / Num. obs: 15420 / % possible obs: 87.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.093
Reflection shellResolution: 1.88→2.02 Å
Reflection
*PLUS
Num. measured all: 226047

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: COORDINATES FROM PDB
Starting model: PDB ID 1RYT

1ryt


Resolution: 1.9→20 Å / Num. parameters: 696 / Num. restraintsaints: 652 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 771 5 %RANDOM
Rwork0.176 ---
all0.197 15420 --
obs0.176 11533 83 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1652
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 3 165 1690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_plane_restr0.02
X-RAY DIFFRACTIONs_chiral_restr0.02

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